In this paper, we take Nature as a case study to present a new method for calculating and analyzing the structure of the Impact Factor (IF) using the Web of Science (WoS) database and the definition of IF. We calculated Natures IF for 2013 using data retrieved on 21 March 2014 from the WoS database and comprehensively analyzed its structural features, thereby identifying the contributions to Natures IF for 2013 of different document types, highly cited papers, highly cited authors, different institutions, and different countries and regions. The results show: (a) the calculated value of Natures IF for 2013 is 41.002 according to data retrieved in March of 2014; (b) two types of document, article and review, made prominent contributions to Natures IF for 2013, with contribution values of 35.338 and 3.179, respectively; (c) the institutions that made the greatest contributions to Natures IF for 2013 are mainly located in the USA and England, with the first three highly cited institutions being Harvard University, Stanford University, and Washington University; (d) the contributions of different countries and regions to Natures IF for 2013 differ greatly, with the combined contribution rate of the USA and England being 70.4 percent.